Kwame Kizito put the Phobians ahead on 57 minutes but Sadick Adams brought the Porcupine Warriors level seven minutes to full time after Leonard Tawiah was adjudged to have handled in the box.
The call has generated enormous debate with Hearts linchpin Winful Cobbinah slamming the match official on live TV after the game.
"It was a very exciting game because both teams came out to play but we felt a little bit ahead of them only that we did not make it count in terms of the final result," Nuttall said.
"But I must congratulate both teams, it was a fantastic game.
"Had we taken our chances in the first half, we could have emerged victors.
"In the second half, they [Kotoko] came out strongly but we were fortunate to get a goal through Kizito.
"To be honest it looked like we were going to run away with the three points but for the controversial penalty."
Hearts, nonetheless, still hold the bragging rights, having won 35, drawn 38 and lost 33 of 106 league meetings with Kotoko.
The Phobians sit third on the league log, just one place above the Porcupine Warriors.